+Open data
-Basic information
Entry | Database: PDB / ID: 1t6t | ||||||
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Title | putative protein from Aquifex aeolicus | ||||||
Components | putative protein | ||||||
Keywords | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / Aquifex aeolicus / PSI / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG | ||||||
Function / homology | Ribonuclease M5-like, TOPRIM domain / Dna Topoisomerase Vi A Subunit; Chain: A, domain 2 / Dna Topoisomerase Vi A Subunit; Chain: A, domain 2 - #10 / TOPRIM / Toprim domain / TOPRIM domain / 3-Layer(aba) Sandwich / Alpha Beta / Toprim domain-containing protein Function and homology information | ||||||
Biological species | Aquifex aeolicus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.8 Å | ||||||
Authors | Cuff, M.E. / Zhou, M. / Collart, F. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG) | ||||||
Citation | Journal: To be Published Title: putative protein from Aquifex aeolicus Authors: Cuff, M.E. / Zhou, M. / Collart, F. / Joachimiak, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1t6t.cif.gz | 61.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1t6t.ent.gz | 48.4 KB | Display | PDB format |
PDBx/mmJSON format | 1t6t.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/t6/1t6t ftp://data.pdbj.org/pub/pdb/validation_reports/t6/1t6t | HTTPS FTP |
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-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 13835.709 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aquifex aeolicus (bacteria) / Strain: VF5 / Gene: NP_214428 / Production host: Escherichia coli (E. coli) / References: UniProt: O67859 #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.6 Å3/Da / Density % sol: 52.5 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7 Details: ethanol, sodium cacodylate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 294K |
-Data collection
Diffraction | Mean temperature: 150 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97885 Å |
Detector | Type: CUSTOM-MADE / Detector: CCD / Date: Dec 21, 2003 / Details: SBC2 |
Radiation | Monochromator: sagitally focussed Si(111) / Protocol: SAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97885 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→26.73 Å / Num. all: 22463 / Num. obs: 22463 / % possible obs: 85.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 18.9 Å2 / Limit h max: 22 / Limit h min: -24 / Limit k max: 29 / Limit k min: -24 / Limit l max: 28 / Limit l min: 0 / Observed criterion F max: 843216.03 / Observed criterion F min: 6.5 |
Reflection shell | Resolution: 1.8→1.87 Å / Redundancy: 3.9 % / Mean I/σ(I) obs: 3.7 / % possible all: 43.6 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.8→26.73 Å / Rfactor Rfree error: 0.006 / Occupancy max: 1 / Occupancy min: 1 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: CNS bulk solvent model used / Bsol: 76.684 Å2 / ksol: 0.415027 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 68.25 Å2 / Biso mean: 24.64 Å2 / Biso min: 8.46 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.8→26.73 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8
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Xplor file |
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